Plot

The game starts off with the final movie scene, in which the Parr family walk out from Dash's race, only for The Underminer to drill out of the ground and begin to monologue on how he will rule the world, as the Incredibles get into their suits and prepare for battle. The game then takes its own storyline, as the Incredibles face off against the Underminer. Frozone comes in and the six Supers face off against the supervillain. Before they can confront him, however, drills and robots come out of the ground like moles in a garden. Mr. Incredible tells his family to stop the drills. Then, Mr. Incredible and Frozone team up and agree to get to the Underminer before he causes any more damage. Along the way, the two Supers fight against robots and avoid things falling out of the sky, thanks to the Underminer's attack (a la, cars, boulders, etc.). The two get to the Underminer's machine, but he quickly escapes underground. Mr. Incredible and Frozone venture underground and fight more robots.

As they continue on, Mr. Incredible and Frozone get to a computer that maps out the Underminer's plans and they learn of the Magnomizer, a machine that he has built which can be a threat to the world (in the form of extreme pollution) if it isn't stopped. In order to stop it, the two Supers must go through the Sludge Station.

Mr. Incredible and Frozone fight through more robots and obstacles in the Sludge Station. They eventually destroy a machine blocking their path, and destroy a wall which leads outside into a snowy, gray part of the underground. They go through it and get into a room where they fight the Magnomizer Guardian and its robot minions. Considering that the Guardian is too high off the ground for Frozone to freeze, Mr. Incredible decides to throw objects (robots, whether they're frozen or not by Frozone, metal boxes, frozen sludge balls launched by either the Guardian itself or one of its Grubbot assistants) towards the Magnomizer Guardian. He apparently does enough to make it unable to shoot out any sludge balls or fire balls, thus disabling it.

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They then take an elevator that leads to the Magnomizer basement, where they figure out that the place is unstable and falling apart without the Magnomizer Guardian. They fight through more robots again and make their way up, avoiding falling from the collapsing stairs that they go up through and still battle off robots. They eventually reach the top roof of the Magnomizer, where the machine itself is. While Mr. Incredible unscrews the bolts that holds down the Magnomizer with his super strength, Frozone uses his powers to keep off the guarding robots. Finally, Mr. Incredible unscrews every bolt holding down the Magnomizer and the entire Magnomizer building starts to blow up. Mr. Incredible and Frozone quickly escape through a tank-like machine, and it falls all the way into a deep, dark pit the machine makes when it falls through the ground.

The Underminer is aware that Mr. Incredible and Frozone have destroyed the Magnomizer and alerts the Crustodian, the head of the Giant Robot Factory, that the two Supers might arrive to the Factory, and the Underminer also tells the Crustodian to hurry the deadline for all 100 of the Underminer's giant robots called the Gilgenbots up to Earth's surface for his final attack on Earth and reign supreme as ruler of the entire planet. The Crustodian alarms every robot in the factory about Mr. Incredible and Frozone's arrival. Finally, the two arrive and fight against even more robots as they travel the Factory, where they destroy three Gilgenbots still in production. Eventually, the two reach the main office where the Crustodian is. And because of the three Gilgenbots' destruction, the Crustodian decides that this is an unacceptable failure and declares that he will destroy the other 96 Gilgenbots to cover his failure (the Underminer already has a Gilgenbot with him). The Supers fight the Crustodian and take down more robots helping him, also accidentally activating the bomb that will blow up the Factory - starting with the office! Eventually, Mr. Incredible and Frozone defeat the Crustodian in battle by destroying his giant robot body and the entire place slowly starts to crumble. The Crustodian, who is really just a glass cylinder with electricity in it to keep it active, begins to leave, as his remaining live head rolls and jumps off a ledge, and Mr. Incredible is obsessed with stopping him. Frozone tells Mr. Incredible they have no time, and Mr. Incredible leaves once the Crustodian disappears. They take an elevator that leads them to an underwater plant that originally supplied power to the now-destroyed Magnomizer, and the still-active Corrupterator.

Mr. Incredible and Frozone figure out they are in a power impressure plant run by a robot named Dug - and the plant is slowly breaking and the water is coming through! After traveling from elevator to elevator and fighting off difficult robots, the two finally reach Dug. Dug tells him he didn't mean to have robots attack the two Supers and he agrees to help them save a group of scientists that are trapped in the Underminer's Corrupterator, a giant machine the size of a major city. On the way the two help protect Dug from robots he can't command, upcoming lasers, deadly obstacles, and gaps. After all this, Dug opens an elevator for Mr. Incredible and Frozone to go into to save the scientists. Unfortunately, Dug refuses to go any further and leaves Mr. Incredible and Frozone on their own, but he tells them that because of his actions, the Corrupterator will simply shut down, and the Underminer has no idea how to reactivate it. Dug will most likely be destroyed because the Gilgenbots' destruction and debris will soon start crashing upon his underwater plant and destroy everything in it.

The Underminer announces to all his robots that even though most of his plans are foiled and the robot army is delayed, Doomsday will come. The robots' next mission is to kill the scientists. But Mr. Incredible and Frozone easily find and save the scientists in the Corrupterator building, but they must keep them from getting killed by lasers. After the scientists are saved, they go down through an escape tunnel and Mr. Incredible and Frozone continue their journey. They eventually confront the Underminer and try to stop him, but the mutant escapes in his Gilgenbot. Mr. Incredible and Frozone then get to an elevator in which they go up to the ground to stop the Underminer once and for all.

Mr. Incredible and Frozone finally come out aboveground, and confront the Underminer, who shows off his only Gilgenbot to Metroville. But first, Mr. Incredible and Frozone must defeat a group of robots the Underminer has for them. After they succeed, the Underminer comes in to attack with another, smaller machine. The two damage the machine, but the Underminer returns to the Gilgenbot to rest while the rest of his machines try to defeat Mr. Incredible and Frozone. The two Supers succeed in taking down the machines and the Underminer returns to fight Mr. Incredible and Frozone. Even though he returned to his machine, he quickly came back with only laser-firing turrets lashing for Mr. Incredible and Frozone to face. In the end, Mr. Incredible and Frozone finally defeat the Underminer, making his machine go haywire, fly into the sky, and come down hard on the Gilgenbot's head, causing a giant explosion that most likely kills the Underminer and destroys the Gilgenbot. Mr. Incredible and Frozone escape the blast and Mr. Incredible's family arrive just in time to watch with Mr. Incredible and Frozone defeat the Underminer and save the world once more.

Trivia

The beginning of Incredibles 2 shows a different version of the events taking place immediately after the first film, contradicting the events of this game. As such, The Incredibles: Rise of the Underminer is seemingly non-canon as is the Incredibles Boom comic series which continues after the events of the game, making those events alternate sequels.